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Magnesium in PDB 5sgy: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide, PDB code: 5sgy was solved by C.Joseph, J.Benz, A.Flohr, J.Peters, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.52 / 2.36
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.313, 135.313, 234.951, 90, 90, 120
R / Rfree (%) 18.2 / 24.1

Other elements in 5sgy:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide (pdb code 5sgy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide, PDB code: 5sgy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sgy

Go back to Magnesium Binding Sites List in 5sgy
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:35.7
occ:1.00
 O A:HOH995 1.8 28.2 1.0
OD1 A:ASP564 1.9 33.6 1.0
O A:HOH953 2.0 27.4 1.0
O A:HOH964 2.0 31.4 1.0
O A:HOH918 2.0 30.2 1.0
O A:HOH915 2.2 32.4 1.0
CG A:ASP564 3.0 34.5 1.0
OD2 A:ASP564 3.4 36.3 1.0
ZN A:ZN801 3.8 39.2 1.0
OE2 A:GLU592 4.0 40.6 1.0
NE2 A:HIS595 4.0 33.2 1.0
O A:HOH986 4.0 38.0 1.0
CD2 A:HIS567 4.1 38.5 1.0
O A:HOH960 4.1 44.5 1.0
O A:HOH970 4.2 50.5 1.0
CB A:ASP564 4.3 32.2 1.0
NE2 A:HIS567 4.3 37.9 1.0
CD2 A:HIS595 4.3 34.4 1.0
CD2 A:HIS563 4.3 31.4 1.0
O A:HIS563 4.4 31.9 1.0
OG1 A:THR633 4.4 35.7 1.0
CD2 A:HIS525 4.6 36.0 1.0
O A:THR633 4.6 35.9 1.0
NE2 A:HIS525 4.6 33.0 1.0
NE2 A:HIS563 4.7 31.2 1.0
CA A:ASP564 4.7 31.7 1.0
OD2 A:ASP674 4.7 52.2 1.0
CG A:GLU592 4.8 35.7 1.0
CD A:GLU592 4.8 38.7 1.0
CB A:THR633 4.9 34.6 1.0

Magnesium binding site 2 out of 4 in 5sgy

Go back to Magnesium Binding Sites List in 5sgy
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:31.1
occ:1.00
 O B:HOH930 1.8 31.1 1.0
O B:HOH948 1.9 25.3 1.0
O B:HOH986 1.9 27.0 1.0
O B:HOH980 2.1 26.1 1.0
O B:HOH904 2.1 23.6 1.0
OD1 B:ASP564 2.2 32.1 1.0
CG B:ASP564 3.2 31.9 1.0
OD2 B:ASP564 3.5 33.2 1.0
O B:HOH995 3.9 53.2 1.0
ZN B:ZN801 3.9 36.7 1.0
OE2 B:GLU592 3.9 32.4 1.0
O B:HOH943 4.1 34.1 1.0
O B:HOH954 4.1 43.7 1.0
NE2 B:HIS595 4.1 35.8 1.0
CD2 B:HIS567 4.2 33.4 1.0
OG1 B:THR633 4.3 31.2 1.0
CD2 B:HIS595 4.3 39.6 1.0
NE2 B:HIS567 4.3 34.1 1.0
CD2 B:HIS563 4.3 31.3 1.0
O B:HIS563 4.4 36.2 1.0
OD2 B:ASP674 4.4 39.4 1.0
O B:THR633 4.5 35.2 1.0
CB B:ASP564 4.5 30.3 1.0
CD2 B:HIS525 4.7 31.6 1.0
CG B:GLU592 4.7 31.5 1.0
NE2 B:HIS563 4.7 32.2 1.0
NE2 B:HIS525 4.7 33.4 1.0
CD B:GLU592 4.7 30.0 1.0
CB B:THR633 4.8 34.9 1.0
CA B:ASP564 4.8 31.8 1.0

Magnesium binding site 3 out of 4 in 5sgy

Go back to Magnesium Binding Sites List in 5sgy
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:31.9
occ:1.00
 O C:HOH963 1.9 33.2 1.0
O C:HOH920 2.0 32.4 1.0
O C:HOH990 2.0 31.0 1.0
OD1 C:ASP564 2.0 29.7 1.0
O C:HOH946 2.0 24.4 1.0
O C:HOH960 2.1 25.4 1.0
CG C:ASP564 3.1 31.7 1.0
OD2 C:ASP564 3.5 35.7 1.0
ZN C:ZN801 3.8 38.8 1.0
NE2 C:HIS595 3.9 38.4 1.0
O C:HOH974 4.0 38.1 1.0
OE2 C:GLU592 4.1 35.0 1.0
CD2 C:HIS567 4.1 32.6 1.0
O C:HOH957 4.2 46.1 1.0
CD2 C:HIS563 4.3 26.9 1.0
NE2 C:HIS567 4.3 35.9 1.0
CD2 C:HIS595 4.3 35.1 1.0
O C:HIS563 4.3 33.9 1.0
OG1 C:THR633 4.4 37.4 1.0
CB C:ASP564 4.4 29.6 1.0
OD2 C:ASP674 4.4 31.1 1.0
NE2 C:HIS563 4.7 29.0 1.0
O C:THR633 4.7 33.7 1.0
CD2 C:HIS525 4.7 39.5 1.0
O C:HOH995 4.8 62.0 1.0
CA C:ASP564 4.8 29.9 1.0
NE2 C:HIS525 4.8 38.8 1.0
CG C:GLU592 4.8 32.7 1.0
CB C:THR633 4.8 33.5 1.0
CD C:GLU592 4.9 34.0 1.0

Magnesium binding site 4 out of 4 in 5sgy

Go back to Magnesium Binding Sites List in 5sgy
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:50.9
occ:1.00
 O D:HOH918 2.0 52.3 1.0
O D:HOH914 2.1 37.7 1.0
OD1 D:ASP564 2.2 52.9 1.0
O D:HOH903 2.2 39.9 1.0
O D:HOH910 2.2 44.9 1.0
O D:HOH902 2.3 46.2 1.0
CG D:ASP564 3.2 50.5 1.0
OD2 D:ASP564 3.5 57.9 1.0
O D:HOH911 3.8 41.5 1.0
ZN D:ZN801 3.9 56.1 1.0
O D:HOH919 3.9 42.6 1.0
CD2 D:HIS567 4.0 51.0 1.0
OE2 D:GLU592 4.0 51.4 1.0
NE2 D:HIS595 4.1 54.7 1.0
NE2 D:HIS567 4.1 54.7 1.0
CD2 D:HIS595 4.4 55.3 1.0
O D:HIS563 4.5 46.2 1.0
CD2 D:HIS563 4.5 48.9 1.0
OG1 D:THR633 4.5 42.3 1.0
CB D:ASP564 4.5 49.6 1.0
CD2 D:HIS525 4.5 59.7 1.0
NE2 D:HIS525 4.6 59.1 1.0
O D:THR633 4.6 55.1 1.0
OD2 D:ASP674 4.8 59.1 1.0
CA D:ASP564 4.8 48.1 1.0
O D:HOH920 4.8 44.2 1.0
NE2 D:HIS563 4.9 47.8 1.0
CD D:GLU592 4.9 52.2 1.0

Reference:

A.Flohr, D.Schlatter, B.Kuhn, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Mon Sep 30 03:52:21 2024

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